Changed common help to remove -names, -filenames, and -sortout from all tools but intersect and closest.

If modification time of a FASTA index file is less than modification
time of its FASTA file, then the warning message is shown; resolves
#228.

Don't rebuild FileRecordTools/FileRecord*.o every time.
Clean version_git.h.

The previous maxVal initialisation elicited a warning; by using unsigned
we can format all values of int including the most negative anyway.

...so that namespace "std" already exists when we try to use it,
as it will have been declared by the standard headers #included.
Doing otherwise elicits a warning from Clang.

Fixed bug where name conventions weren't tested for unsorted data; stopped namecheck on unmapped bam records

corected unit test files for VCF insertions; changed to min instead of max for SV's with multiple vals

Corrected bug 218 by disabling intra-file name convention checking and allowing -nonamecheck for unsorted files